The clinical course of inflammatory bowel diseases (IBDs) is variable. The best outcomes include only a 65% rate of sustained remission—in other words, at least 35% of patients receiving standardized care will experience at least one relapse over the course of a year (Crandall W V, et al. Pediatrics 2012; 129:e1030-41; Samson C M, et al. J Pediatr Gastroenterol Nutr 2012; 55:679-88). Approximately 15% of patients ultimately do not respond to medical therapy and require surgery for stricturing/penetrating behavior within three years of diagnosis (Siegel C A, et al. Inflamm Bowel Dis 2011; 17:30-8). These varied outcomes are likely due to substantial genetic, microbial, and immune heterogeneity in disease pathogenesis (Sartor R B. Nat Clin Pract Gastroenterol Hepatol 2006; 3:390-407). Clinical tools and biomarkers to define important patient subsets are lacking. While earlier use of anti-tumor necrosis factor (TNF) therapy is likely to improve rates of sustained remission and reduce rates of surgery, there are currently no diagnostic tools with sufficient accuracy to predict either relapse, structuring, or continued remission, and thereby guide selection of appropriate therapies, such as introduction of anti-TNF when it is likely to provide the greatest benefit (Colombel J F, et al. N Engl J Med 2010; 362:1383-95).